bims-ectoca 2022-02-13 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2022–02–13
ten papers selected by
Ankita Daiya, Birla Institute of Technology and Science

A CTCF-Binding Element and Histone Deacetylation Cooperatively Maintain Chromatin Loops, Linking to Long-Range Gene Regulation in Cancer Genomes.
The Epigenetic Regulation of OLIG2 by Histone Demethylase KDM6B in Glioma Cells.
Discovery and Mechanism of Small Molecule Inhibitors Selective for the Chromatin-Binding Domains of Oncogenic UHRF1.
The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium.
The synergistic anticancer effect of the bromodomain inhibitor OTX015 and histone deacetylase 6 inhibitor WT-161 in osteosarcoma.
Prudent application of single-cell RNA sequencing in understanding cellular features and functional phenotypes in cancer studies.
Combined inhibition of G9a and EZH2 suppresses tumor growth via synergistic induction of IL24-mediated apoptosis.
Enhancer RNA LINC00242-Induced Expression of PHF10 Drives a Better Prognosis in Pancreatic Adenocarcinoma.
TEAD4 nuclear localization and regulation by miR-4269 and miR-1343-3p in colorectal carcinoma.
Temporal analyses of postnatal liver development and maturation by single-cell transcriptomics.

Front Oncol. 2021 ;11 821495

A CTCF-Binding Element and Histone Deacetylation Cooperatively Maintain Chromatin Loops, Linking to Long-Range Gene Regulation in Cancer Genomes.

Ran Tang, Yiqun Li, Fang Han, Zhenzhi Li, Xiaoyu Lin, Haoxiu Sun, Xiaoqing Zhang, Qinghua Jiang, Huan Nie, Yu Li.

   Background: Genes spanning long chromosomal domains are coordinately regulated in human genome, which contribute to global gene dysregulation and carcinogenesis in cancer. It has been noticed that epigenetic modification and chromatin architecture may participate in the regulation process. However, the regulation patterns and functional elements of long-range gene regulation are unclear.
Methods: Based on the clinical transcriptome data from different tumor sets, a novel expressional correlation analysis pipeline was performed to classify the co-regulated regions and subsets of intercorrelated regions. The GLAM2 program was used to predict conserved DNA elements that enriched in regions. Two conserved elements were selected to delete in Ishikawa and HeLa cells by CRISPR-Cas9. SAHA treatment and HDAC knockdown were used to change the histone acetylation status. Using qPCR, MTT, and scratch healing assay, we evaluate the effect on gene expression and cancer cell phenotype. By DNA pull-down and ChIP, the element-binding proteins were testified. 3C and 3D-FISH were performed to depict the alteration in chromatin architecture.
Results: In multiple cancer genomes, we classified subsets of coordinately regulated regions (sub-CRRs) that possibly shared the same regulatory mechanisms and exhibited similar expression patterns. A new conserved DNA element (CRE30) was enriched in sub-CRRs and associated with cancer patient survival. CRE30 could restrict gene regulation in sub-CRRs and affect cancer cell phenotypes. DNA pull-down showed that multiple proteins including CTCF were recruited on the CRE30 locus, and ChIP assay confirmed the CTCF-binding signals. Subsequent results uncovered that as an essential element, CRE30 maintained chromatin loops and mediated a compact chromatin architecture. Moreover, we found that blocking global histone deacetylation induced chromatin loop disruption and CTCF dropping in the region containing CRE30, linked to promoted gene regulation. Additionally, similar effects were observed with CRE30 deletion in another locus of chromosome 8.
Conclusions: Our research clarified a new functional element that recruits CTCF and collaborates with histone deacetylation to maintain high-order chromatin organizations, linking to long-range gene regulation in cancer genomes. The findings highlight a close relationship among conserved DNA element, epigenetic modification, and chromatin architecture in long-range gene regulation process.

Keywords:  CTCF; cancer genome; chromatin loops; functional DNA element; histone deacetylation

DOI:  https://doi.org/10.3389/fonc.2021.821495
J Mol Neurosci. 2022 Feb 07.

The Epigenetic Regulation of OLIG2 by Histone Demethylase KDM6B in Glioma Cells.

Aixia Sui, Biaogang Han, Wenjun Ren, Weiliang He, Chao Gao, Xiaohui Han, Shifeng Liu, Yan Zhang, Xueling Qi, Xiaoqiang Guo.

  Gliomas are common tumors that occur in the brain, accounting for 80% of all malignant brain tumors. Oligodendrocyte transcription factor 2 (OLIG2) is a key transcription factor and strongly expressed in gliomas, which drives proliferation and invasion of glioma cells. Our previous studies have shown that histone lysine (K) demethylase 6B (KDM6B) promotes glioma development. The data also showed that OLIG2 content was positively correlated with KDM6B. Based on this, we proposed that KDM6B may play biological roles by regulating OLIG2 expression. Subsequently, many experiments were performed including specific inhibitor treatment, gene knockdown, and chromatin immunoprecipitation (ChIP) array. These results indicated that inhibition of KDM6B enzymatic activity with GSK-J4 reduces OLIG2 gene expression and protein content. The KDM6B knockdown experiment yielded similar results, that is, it reduces the mRNA and protein level of OLIG2 in glioma cells. ChIP assay showed that the promoter of OLIG2 can be bound by KDM6B, which catalyzes the demethylation of H3K27me3 and increases the expression of OLIG2. This study reveals a new regulatory mechanism of OLIG2 by KDM6B, which has important implications for the future development of drugs for gliomas and other neurological diseases.

Keywords:  Gliomas; Histone demethylase; KDM6B; OLIG2

DOI:  https://doi.org/10.1007/s12031-022-01976-1
Biochemistry. 2022 Feb 10.

Discovery and Mechanism of Small Molecule Inhibitors Selective for the Chromatin-Binding Domains of Oncogenic UHRF1.

Wallace H Liu, Robert E Miner, Brittany N Albaugh, Gene E Ananiev, Scott A Wildman, John M Denu.

Chromatin abnormalities are common hallmarks of cancer cells, which exhibit alterations in DNA methylation profiles that can silence tumor suppressor genes. These epigenetic patterns are partly established and maintained by UHRF1 (ubiquitin-like PHD and RING finger domain-containing protein 1), which senses existing methylation states through multiple reader domains, and reinforces the modifications through recruitment of DNA methyltransferases. Small molecule inhibitors of UHRF1 would be important tools to illuminate molecular functions, yet no compounds capable of blocking UHRF1-histone binding in the context of the full-length protein exist. Here, we report the discovery and mechanism of action of compounds that selectively inhibit the UHRF1-histone interaction with low micromolar potency. Biochemical analyses reveal that these molecules are the first inhibitors to target the PHD finger of UHRF1, specifically disrupting histone H3 arginine 2 interactions with the PHD finger. Importantly, this unique inhibition mechanism is sufficient to displace binding of full-length UHRF1 with histones in vitro and in cells. Together, our study provides insight into the critical role of the PHD finger in driving histone interactions, and demonstrates that targeting this domain through a specific binding pocket is a tractable strategy for UHRF1-histone inhibition.

DOI: https://doi.org/10.1021/acs.biochem.1c00698
Nucleic Acids Res. 2022 Feb 07. pii: gkac047. [Epub ahead of print]

The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium.

Ngai Ting Chan, Junfeng Huang, Gui Ma, Hao Zeng, Kristine Donahue, Yidan Wang, Lingjun Li, Wei Xu.

CTR9 is the scaffold subunit in polymerase-associated factor complex (PAFc), a multifunctional complex employed in multiple steps of RNA Polymerase II (RNAPII)-mediated transcription. CTR9/PAFc is well known as an evolutionarily conserved elongation factor that regulates gene activation via coupling with histone modifications enzymes. However, little is known about its function to restrain repressive histone markers. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the H3K27me3 levels are strictly controlled by CTR9. Quantitative profiling of histone modifications revealed a striking increase of H3K27me3 levels upon loss of CTR9. Moreover, loss of CTR9 leads to genome-wide expansion of H3K27me3, as well as increased recruitment of PRC2 on chromatin, which can be reversed by CTR9 restoration. Further, CTR9 depletion triggers a PRC2 subtype switch from the less active PRC2.2, to the more active PRC2.1 with higher methyltransferase activity. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution provide a unique mechanism that explains the transition from transcriptionally active chromatin states to repressive chromatin states and sheds light on the biological functions of CTR9 in development and cancer.

DOI: https://doi.org/10.1093/nar/gkac047
Cancer Cell Int. 2022 Feb 08. 22(1): 64

The synergistic anticancer effect of the bromodomain inhibitor OTX015 and histone deacetylase 6 inhibitor WT-161 in osteosarcoma.

Bo Yu, Lang Liu, Feng Cai, Yuanxiang Peng, Xiaofeng Tang, Duo Zeng, Teng Li, Feifei Zhang, Yiping Liang, Xuhui Yuan, Jiayu Li, Zhengzai Dai, Qi Liao, Xiao-Bin Lv.

   BACKGROUND: Osteosarcoma (OS) is a tumour with a high malignancy level and a poor prognosis. First-line chemotherapy for OS has not been improved for many decades. Bromodomain and extraterminal domain (BET) and histone deacetylases (HDACs) regulate histone acetylation in tandem, and BET and HDACs have emerged as potential cancer therapeutic targets.
METHODS: Cell proliferation, migration, invasion, colony formation, and sphere-forming assays were performed with the two inhibitors alone or in combination to evaluate their suppressive effect on the malignant properties of OS cells. Apoptosis and the cell cycle profile were measured by flow cytometry. The synergistic inhibitory effect of OTX015/WT-161 on tumours was also examined in a nude mouse xenograft model.
RESULTS: The combined therapy of OTX015/WT-161 synergistically inhibited growth, migration, and invasion and induced apoptosis, resulting in G1/S arrest of OS cells. Additionally, OTX015/WT-161 inhibited the self-renewal ability of OS stem cells (OSCs) in a synergistic manner. Further mechanistic exploration revealed that the synergistic downregulation of β-catenin by OTX015-mediated suppression of FZD2 and WT-161-mediated upregulation of PTEN may be critical for the synergistic effect. Finally, the results of an in vivo assay showed that tumour xenografts were significantly decreased after treatment with the OTX015/WT-161 combination compared with OTX015 or WT-161 alone.
CONCLUSIONS: Our findings in this study demonstrated that OTX015 and WT-161 had synergistic anticancer efficacy against OS, and their combination might be a promising therapeutic strategy for OS.

Keywords:  OTX015; Osteosarcoma; Synergistic efficacy; WT-161; β-Catenin

DOI:  https://doi.org/10.1186/s12935-022-02443-y
Chin J Cancer Res. 2021 Dec 31. 33(6): 719-723

Prudent application of single-cell RNA sequencing in understanding cellular features and functional phenotypes in cancer studies.

Xuanhao Xu, Zemin Zhang.

  This decade has seen remarkable advances in the field of high-throughput single cell techniques. Single-cell RNA sequencing (scRNA-seq) has proven to be a powerful strategy to study the heterogeneity in clinical samples, providing an unbiased approach to uncover the characteristics in different cell subsets. To ensure the reproducibility and robustness of biological discoveries, researchers need to be aware of hidden caveats in tissue dissociation, cell capturing and transcripts measurement which may affect cell composition assessment and cellular function annotation. With measured interpretation of data and innovations in experimental and technical approaches, scRNA-seq can greatly unravel the heterogeneity in complex system and improve our understandings in tissue homeostasis and cancer biology.

Keywords:  Single-cell RNA sequencing; cancer study; immune cells; tumor microenvironment

DOI:  https://doi.org/10.21147/j.issn.1000-9604.2021.06.08
Cancer Res. 2022 Feb 11. pii: canres.2218.2021. [Epub ahead of print]

Combined inhibition of G9a and EZH2 suppresses tumor growth via synergistic induction of IL24-mediated apoptosis.

Francesco Casciello, Gregory M Kelly, Priya Ramarao-Milne, Nabilah Kamal, Teneale A Stewart, Pamela Mukhopadhyay, Stephen H Kazakoff, Mariska Miranda, Dorim Kim, Felicity M Davis, Nicholas K Hayward, Paula M Vertino, Nicola Waddell, Frank Gannon, Jason S Lee.

G9a and EZH2 are two histone methyltransferases commonly upregulated in several cancer types, yet the precise roles that these enzymes play cooperatively in cancer is unclear. We demonstrate here that frequent concurrent upregulation of both G9a and EZH2 occurs in several human tumors. These methyltransferases cooperatively repressed molecular pathways responsible for tumor cell death. In genetically distinct tumor subtypes, concomitant inhibition of G9a and EZH2 potently induced tumor cell death, highlighting the existence of tumor cell survival dependency at the epigenetic level. G9a and EZH2 synergistically repressed expression of genes involved in the induction of endoplasmic reticulum (ER) stress and the production of reactive oxygen species. IL24 was essential for the induction of tumor cell death and was identified as a common target of G9a and EZH2. Loss-of-function of G9a and EZH2 activated the IL24-ER stress axis and increased apoptosis in cancer cells while not affecting normal cells. These results indicate that G9a and EZH2 promotes the evasion of ER stress-mediated apoptosis by repressing IL24 transcription, therefore suggesting that their inhibition may represent a potential therapeutic strategy for solid cancers.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-2218
Front Oncol. 2021 ;11 795090

Enhancer RNA LINC00242-Induced Expression of PHF10 Drives a Better Prognosis in Pancreatic Adenocarcinoma.

Wen Tong, Liuyang Zhu, Yi Bai, Long Yang, Zirong Liu, Yamin Zhang.

  Enhancer RNA is a kind of non-coding RNA, which is transcribed from the enhancer region of gene and plays an important role in gene transcription regulation. However, the role of eRNA in pancreatic adenocarcinoma (PAAD) is still unclear. In this study, we identified the key eRNA and its target gene in PAAD. The transcriptome data and clinical information of pancreatic cancer were downloaded from the UCSC Xena platform. A total of 2,695 eRNAs and its target gene predicted by the PreSTIGE method were selected as candidate eRNA-target pairs. After survival analysis, we found that LINC00242 was the eRNA most related to patients' survival, and correlation analysis further indicated that LINC00242 and its target gene PHF10 had a significant co-expression relationship. Downregulation of LINC00242 was significantly associated with unfavorable clinicopathological features. Based on pan-cancer analysis, we found that LINC00242 was associated with the survival of multiple cancers, and LINC00242 was co-expressed with its target genes in multiple cancer types. External experiments further demonstrated that PHF10 was the downstream target gene of LINC00242. After ssGSEA analysis, PAAD patients were classified as high, medium, and low immune cell infiltration clusters. Compared with the low and medium immune infiltration clusters, the expression level of PHF10 was significantly upregulated in the high immune infiltration clusters. After performing the CIBERSORT algorithm, we found that there was a significant difference in the abundance of immune infiltrating cells between the PHF10 high- and low-expression groups. Additionally, the web tool TIMER was used to detect the distribution and expression of PHF10 in pan-cancer.

Keywords:  LINC00242; PHF10; biomarker; enhancer RNA; pancreatic cancer

DOI:  https://doi.org/10.3389/fonc.2021.795090
Pathol Res Pract. 2022 Jan 29. pii: S0344-0338(22)00034-6. [Epub ahead of print]231 153791

TEAD4 nuclear localization and regulation by miR-4269 and miR-1343-3p in colorectal carcinoma.

Ishrat Parveiz Bhat, Tahseen Bilal Rather, Gulzar A Bhat, Irfan Maqbool, Kulsum Akhtar, Gowhar Rashid, Fazl Q Parray, Syed Besina, Syed Mudassar.

   BACKGROUND AND AIMS: TEAD4 transcription factor belonging to TEAD-family, is a key downstream element of the Hippo Signalling pathway and is very important for YAPinduced tumor progression. YAP-TEAD interaction is required to promote tumor progression and metastasis in various cancers. This study aims to investigate the role of TEAD4 in CRC progression and to compare the TEAD4 expression with different clinicopathological parameters of the study population. We also aim to explore the expression pattern of miR-4269 and miR-1343-3p and their functional role in TEAD4 mediated CRC progression. Furthermore, we intend to evaluate the prognostic significance of TEAD4, miR-4269, and miR-1343-3p in colorectal carcinoma.
METHODS: Real-time PCR, Immunohistochemical Staining, and Western Blotting were performed on 71 human CRC tissue specimens and their adjacent normal tissues to evaluate the TEAD4 expression and the results were statistically analyzed against the clinicopathological variables of patient data and also with survival data using STATA software. miRNA expression was analyzed by quantitative real-time PCR.
RESULTS: TEAD4 expression levels in tumor specimens were significantly higher than their paired normal specimens. The higher protein expression levels showed a significant association with TNM stage, Duke Stage, tumor grade, invasion depth, node status, necrosis of tumor tissue, lymphovascular and perineural invasion. As per the cox-regression model and classification tree analysis, TNM stage and perineural invasion were important predictors for TEAD4 expression and prognosis of CRC patients. Survival analysis indicated that TEAD4 overexpression was associated with poorer overall and disease-free survival. miR-4269 and miR-1343-3p were downregulated in CRC tumors and showed a negative correlation with TEAD4. The nuclear overexpressed TEAD4 and downregulated miR-4269 and miR-1343-3p evaluated for the first time in CRC, are believed to serve as important prognostic markers in CRC.
CONCLUSION: Expression of TEAD4 was increased in CRC and was negatively regulated by miR-4269 and miR-1343-3p. The overexpression of TEAD4 is linked with poor overall and disease-free survival of CRC patients. These findings support prior observations and thus TEAD4 may be a possible prognostic marker in CRC.

Keywords:  Colorectal cancer; Immunohistochemistry; Quantitative real time PCR; TEAD4; Western blotting

DOI:  https://doi.org/10.1016/j.prp.2022.153791
Dev Cell. 2022 Feb 07. pii: S1534-5807(22)00004-1. [Epub ahead of print]57(3): 398-414.e5

Temporal analyses of postnatal liver development and maturation by single-cell transcriptomics.

Yan Liang, Kota Kaneko, Bing Xin, Jin Lee, Xin Sun, Kun Zhang, Gen-Sheng Feng.

  The postnatal development and maturation of the liver, the major metabolic organ, are inadequately understood. We have analyzed 52,834 single-cell transcriptomes and identified 31 cell types or states in mouse livers at postnatal days 1, 3, 7, 21, and 56. We observe unexpectedly high levels of hepatocyte heterogeneity in the developing liver and the progressive construction of the zonated metabolic functions from pericentral to periportal hepatocytes, which is orchestrated with the development of sinusoid endothelial, stellate, and Kupffer cells. Trajectory and gene regulatory analyses capture 36 transcription factors, including a circadian regulator, Bhlhe40, in programming liver development. Remarkably, we identified a special group of macrophages enriched at day 7 with a hybrid phenotype of macrophages and endothelial cells, which may regulate sinusoidal construction and Treg-cell function. This study provides a comprehensive atlas that covers all hepatic cell types and is instrumental for further dissection of liver development, metabolism, and disease.

Keywords:  construction of metabolic zones; endothelial cells; functional maturation of liver; hepatocyte heterogeneity; interaction of macrophages; postnatal liver development; single cell transcriptomics

DOI:  https://doi.org/10.1016/j.devcel.2022.01.004